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mkdocs.yml
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mkdocs.yml
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site_name: Sopa
repo_name: gustaveroussy/sopa
repo_url: https://github.com/gustaveroussy/sopa
copyright: Copyright © 2023 - 2024 Quentin Blampey
theme:
name: material
logo: assets/sopa_small_white.png
favicon: assets/sopa_favicon.png
features:
- content.code.annotate
nav:
- Home: index.md
- Getting Started: getting_started.md
- Tutorials:
- Snakemake pipeline: tutorials/snakemake.md
- CLI usage: tutorials/cli_usage.md
- API usage: tutorials/api_usage.ipynb
- Explorer usage: tutorials/xenium_explorer/explorer.ipynb
- Align images (e.g. H&E): tutorials/align.md
- Spatial statistics: tutorials/spatial.ipynb
- H&E usage: tutorials/he.ipynb
- Advanced segmentation: tutorials/advanced_segmentation.md
- Other segmentation methods:
- ComSeg: tutorials/comseg.ipynb
- CLI: cli.md
- API:
- sopa.spatial: api/spatial.md
- sopa.segmentation:
- sopa.segmentation.shapes: api/segmentation/shapes.md
- sopa.segmentation.aggregate: api/segmentation/aggregate.md
- sopa.segmentation.stainings: api/segmentation/stainings.md
- sopa.segmentation.transcripts: api/segmentation/transcripts.md
- sopa.segmentation.methods: api/segmentation/methods.md
- sopa.segmentation.patching: api/segmentation/patching.md
- sopa.segmentation.tissue: api/segmentation/tissue.md
- sopa.io: api/io.md
- sopa.annotation: api/annotation.md
- sopa.utils:
- sopa.utils.image: api/utils/image.md
- sopa.utils.polygon_crop: api/utils/polygon_crop.md
- sopa.patches: api/patches.md
- sopa._sdata: api/_sdata.md
- Frequently asked questions: faq.md
- Cite us: cite_us.md
plugins:
- search
- mkdocstrings:
handlers:
python:
options:
show_root_heading: true
heading_level: 3
- mkdocs-jupyter:
include_source: True
markdown_extensions:
- admonition
- attr_list
- md_in_html
- pymdownx.details
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences
- pymdownx.arithmatex:
generic: true
- pymdownx.tabbed:
alternate_style: true
extra_css:
- css/termynal.css
- css/custom.css
extra_javascript:
- js/termynal.js
- js/custom.js
- js/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js